public void contextInitialized(ServletContextEvent sce) {
try {
ServletContext ctx = sce.getServletContext();
// If the DATA_DIR directory doesn't exist no migration check will be done.
// This is a normal situation for Vitro.
File updateDirectory = new File(ctx.getRealPath(DATA_DIR));
if (!updateDirectory.exists()) {
log.debug(
"Directory "
+ ctx.getRealPath(DATA_DIR)
+ " does not exist, no migration check will be attempted.");
return;
}
String logFileName = DATA_DIR + LOG_DIR + timestampedFileName("knowledgeBaseUpdate", "log");
String errorLogFileName =
DATA_DIR + LOG_DIR + timestampedFileName("knowledgeBaseUpdate.error", "log");
UpdateSettings settings = new UpdateSettings();
settings.setAskUpdatedQueryFile(getAskUpdatedQueryPath(ctx));
settings.setDataDir(ctx.getRealPath(DATA_DIR));
settings.setSparqlConstructAdditionsDir(ctx.getRealPath(SPARQL_CONSTRUCT_ADDITIONS_DIR));
settings.setSparqlConstructDeletionsDir(ctx.getRealPath(SPARQL_CONSTRUCT_DELETIONS_DIR));
settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
settings.setSuccessAssertionsFile(ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
settings.setSuccessRDFFormat(SUCCESS_RDF_FORMAT);
settings.setLogFile(ctx.getRealPath(logFileName));
settings.setErrorLogFile(ctx.getRealPath(errorLogFileName));
settings.setAddedDataFile(ctx.getRealPath(ADDED_DATA_FILE));
settings.setRemovedDataFile(ctx.getRealPath(REMOVED_DATA_FILE));
WebappDaoFactory wadf = (WebappDaoFactory) ctx.getAttribute("webappDaoFactory");
settings.setDefaultNamespace(wadf.getDefaultNamespace());
settings.setAssertionOntModelSelector(ModelContext.getBaseOntModelSelector(ctx));
settings.setInferenceOntModelSelector(ModelContext.getInferenceOntModelSelector(ctx));
settings.setUnionOntModelSelector(ModelContext.getUnionOntModelSelector(ctx));
boolean tryMigrateDisplay = true;
try {
settings.setDisplayModel(ModelContext.getDisplayModel(ctx));
OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
settings.setOldTBoxModel(oldTBoxModel);
OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));
settings.setNewTBoxModel(newTBoxModel);
OntModel oldTBoxAnnotationsModel =
loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_ANNOTATIONS_DIR));
settings.setOldTBoxAnnotationsModel(oldTBoxAnnotationsModel);
OntModel newTBoxAnnotationsModel =
loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_ANNOTATIONS_DIR));
settings.setNewTBoxAnnotationsModel(newTBoxAnnotationsModel);
// Display model tbox and display metadata
// old display model tbox model
OntModel oldDisplayModelTboxModel =
loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_TBOX_PATH));
settings.setOldDisplayModelTboxModel(oldDisplayModelTboxModel);
// new display model tbox model
OntModel newDisplayModelTboxModel =
loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_TBOX_PATH));
settings.setNewDisplayModelTboxModel(newDisplayModelTboxModel);
// old display model display model metadata
OntModel oldDisplayModelDisplayMetadataModel =
loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_DISPLAYMETADATA_PATH));
settings.setOldDisplayModelDisplayMetadataModel(oldDisplayModelDisplayMetadataModel);
// new display model display model metadata
OntModel newDisplayModelDisplayMetadataModel =
loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_DISPLAYMETADATA_PATH));
settings.setNewDisplayModelDisplayMetadataModel(newDisplayModelDisplayMetadataModel);
// Get new display model
OntModel newDisplayModelFromFile =
loadModelFromFile(ctx.getRealPath(NEW_DISPLAYMODEL_PATH));
settings.setNewDisplayModelFromFile(newDisplayModelFromFile);
OntModel loadedAtStartupFiles =
loadModelFromDirectory(ctx.getRealPath(LOADED_STARTUPT_DISPLAYMODEL_DIR));
settings.setLoadedAtStartupDisplayModel(loadedAtStartupFiles);
OntModel oldDisplayModelVivoListView =
loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
} catch (Exception e) {
log.info(
"unable to read display model migration files, display model not migrated. "
+ e.getMessage());
tryMigrateDisplay = false;
}
try {
KnowledgeBaseUpdater ontologyUpdater = new KnowledgeBaseUpdater(settings);
try {
if (ontologyUpdater.updateRequired(ctx)) {
ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
ontologyUpdater.update(ctx);
if (tryMigrateDisplay) {
try {
migrateDisplayModel(settings);
log.info("Migrated display model");
} catch (Exception e) {
log.warn("unable to successfully update display model: " + e.getMessage());
}
}
}
} catch (Exception ioe) {
String errMsg = "Exception updating knowledge base " + "for ontology changes: ";
// Tomcat doesn't always seem to print exceptions thrown from
// context listeners
System.out.println(errMsg);
ioe.printStackTrace();
throw new RuntimeException(errMsg, ioe);
}
} catch (Throwable t) {
log.warn("warning", t);
}
} catch (Throwable t) {
t.printStackTrace();
}
}
@Override
public void contextInitialized(ServletContextEvent sce) {
try {
// set up Pellet reasoning for the TBox
OntModelSelector assertionsOms =
ModelContext.getBaseOntModelSelector(sce.getServletContext());
OntModelSelector inferencesOms =
ModelContext.getInferenceOntModelSelector(sce.getServletContext());
OntModelSelector unionOms = ModelContext.getUnionOntModelSelector(sce.getServletContext());
WebappDaoFactoryJena wadf =
(WebappDaoFactoryJena) sce.getServletContext().getAttribute("webappDaoFactory");
if (!assertionsOms
.getTBoxModel()
.getProfile()
.NAMESPACE()
.equals(OWL.NAMESPACE.getNameSpace())) {
log.error("Not connecting Pellet reasoner - the TBox assertions model is not an OWL model");
return;
}
// Set various Pellet options for incremental consistency checking, etc.
PelletOptions.DL_SAFE_RULES = true;
PelletOptions.USE_COMPLETION_QUEUE = true;
PelletOptions.USE_TRACING = true;
PelletOptions.TRACK_BRANCH_EFFECTS = true;
PelletOptions.USE_INCREMENTAL_CONSISTENCY = true;
PelletOptions.USE_INCREMENTAL_DELETION = true;
PelletListener pelletListener =
new PelletListener(
unionOms.getTBoxModel(),
assertionsOms.getTBoxModel(),
inferencesOms.getTBoxModel(),
ReasonerConfiguration.DEFAULT);
sce.getServletContext().setAttribute("pelletListener", pelletListener);
sce.getServletContext().setAttribute("pelletOntModel", pelletListener.getPelletModel());
if (wadf != null) {
wadf.setPelletListener(pelletListener);
}
log.info("Pellet reasoner connected for the TBox");
// set up simple reasoning for the ABox
ServletContext ctx = sce.getServletContext();
BasicDataSource bds = JenaDataSourceSetupBase.getApplicationDataSource(ctx);
String dbType =
ConfigurationProperties.getBean(ctx)
.getProperty( // database type
"VitroConnection.DataSource.dbtype", "MySQL");
Model rebuildModel =
JenaDataSourceSetupBase.makeDBModel(
bds,
JENA_INF_MODEL_REBUILD,
JenaDataSourceSetupBase.DB_ONT_MODEL_SPEC,
TripleStoreType.SDB,
dbType,
ctx);
Model scratchModel =
JenaDataSourceSetupBase.makeDBModel(
bds,
JENA_INF_MODEL_SCRATCHPAD,
JenaDataSourceSetupBase.DB_ONT_MODEL_SPEC,
TripleStoreType.SDB,
dbType,
ctx);
// the simple reasoner will register itself as a listener to the ABox assertions
SimpleReasoner simpleReasoner =
new SimpleReasoner(
unionOms.getTBoxModel(),
assertionsOms.getABoxModel(),
inferencesOms.getABoxModel(),
rebuildModel,
scratchModel);
sce.getServletContext().setAttribute(SimpleReasoner.class.getName(), simpleReasoner);
StartupStatus ss = StartupStatus.getBean(ctx);
List<ReasonerPlugin> pluginList = new ArrayList<ReasonerPlugin>();
List<String> pluginClassnameList = this.readFileOfListeners(ctx);
for (String classname : pluginClassnameList) {
try {
ReasonerPlugin plugin =
(ReasonerPlugin) Class.forName(classname).getConstructors()[0].newInstance();
pluginList.add(plugin);
} catch (Throwable t) {
ss.info(this, "Could not instantiate reasoner plugin " + classname);
}
}
simpleReasoner.setPluginList(pluginList);
if (isRecomputeRequired(sce.getServletContext())) {
log.info("ABox inference recompute required.");
waitForTBoxReasoning(pelletListener);
if (JenaDataSourceSetupBase.isFirstStartup()) {
simpleReasoner.recompute();
} else {
log.info("starting ABox inference recompute in a separate thread.");
new Thread(new ABoxRecomputer(simpleReasoner), "ABoxRecomputer").start();
}
} else if (isMSTComputeRequired(sce.getServletContext())) {
log.info("mostSpecificType computation required. It will be done in a separate thread.");
waitForTBoxReasoning(pelletListener);
new Thread(new MostSpecificTypeRecomputer(simpleReasoner), "MostSpecificTypeComputer")
.start();
}
SimpleReasonerTBoxListener simpleReasonerTBoxListener =
new SimpleReasonerTBoxListener(simpleReasoner);
sce.getServletContext()
.setAttribute(SimpleReasonerTBoxListener.class.getName(), simpleReasonerTBoxListener);
assertionsOms.getTBoxModel().register(simpleReasonerTBoxListener);
inferencesOms.getTBoxModel().register(simpleReasonerTBoxListener);
log.info("Simple reasoner connected for the ABox");
} catch (Throwable t) {
t.printStackTrace();
}
}